Human peripheral blood mononuclear cells (PBMCs) represent a highly responsive primary tissue that is composed of innate and adaptive immune cells. In this study, we compared modulation of the transcriptome of PBMCs by the vitamin D metabolites 25-hydroxyvitamin D-3 (25(OH)D-3), 25(OH)D-2 and 1 alpha,25-dihydroxyvitamin D-3 (1,25(OH)(2)D-3). Saturating concentrations of 1,25(OH)(2)D-3, 25(OH)D-3 and 25(OH)D-2 resulted after 24 h stimulation in a comparable number and identity of target genes, but below 250 nM 25(OH)D-3 and 25(OH)D-2 were largely insufficient to affect the transcriptome. The average EC50 values of 206 common target genes were 322 nM for 25(OH)D-3 and 295 nM for 25(OH)D-2 being some 600-fold higher than 0.48 nM for 1,25(OH)(2)D-3. The type of target gene, such as primary/secondary, direct/indirect or up-/down-regulated, had no significant effect on vitamin D metabolite sensitivity, but individual genes could be classified into high, mid and lower responders. Since the 1 alpha-hydroxylase CYP27B1 is very low expressed in PBMCs and early (4 and 8 h) transcriptome responses to 25(OH)D-3 and 25(OH)D-2 were as prominent as to 1,25(OH)(2)D-3, both vitamin D metabolites may directly control gene expression. In conclusion, at supra-physiological concentrations 25(OH)D-3 and 25(OH)D-2 are equally potent in modulating the transcriptome of PBMCs possibly by directly activating the vitamin D receptor.